add kwargs back again (e844cdce) · Commits · 钟慕尧 / deepchem

deepchem/feat/base_classes.py

+14 −14

Original line number	Diff line number	Diff line
		@@ -24,7 +24,7 @@ class Featurizer(object):
		"""

		def featurize(self, datapoints: Iterable[Any],
		log_every_n: int = 1000) -> np.ndarray:
		log_every_n: int = 1000, **kwargs) -> np.ndarray:
		"""Calculate features for datapoints.

		Parameters
		@@ -47,7 +47,7 @@ class Featurizer(object):
		if i % log_every_n == 0:
		logger.info("Featurizing datapoint %i" % i)
		try:
		features.append(self._featurize(point))
		features.append(self._featurize(point), **kwargs)
		except:
		logger.warning(
		"Failed to featurize datapoint %d. Appending empty array")
		@@ -55,7 +55,7 @@ class Featurizer(object):

		return np.asarray(features)

		def __call__(self, datapoints: Iterable[Any]):
		def __call__(self, datapoints: Iterable[Any], **kwargs):
		"""Calculate features for datapoints.

		`**kwargs` will get passed directly to `Featurizer.featurize`
		@@ -65,9 +65,9 @@ class Featurizer(object):
		datapoints: Iterable[Any]
		Any blob of data you like. Subclasss should instantiate this.
		"""
		return self.featurize(datapoints)
		return self.featurize(datapoints, **kwargs)

		def _featurize(self, datapoint: Any):
		def _featurize(self, datapoint: Any, **kwargs):
		"""Calculate features for a single datapoint.

		Parameters
		@@ -157,7 +157,7 @@ class ComplexFeaturizer(Featurizer):

		def featurize(self,
		complexes: Iterable[Tuple[str, str]],
		log_every_n: int = 100) -> np.ndarray:
		log_every_n: int = 100, **kwargs) -> np.ndarray:
		"""
		Calculate features for mol/protein complexes.

		@@ -181,7 +181,7 @@ class ComplexFeaturizer(Featurizer):
		if idx % log_every_n == 0:
		logger.info("Featurizing datapoint %i" % idx)
		try:
		features.append(self._featurize(point))
		features.append(self._featurize(point, **kwargs))
		successes.append(idx)
		except:
		logger.warning(
		@@ -204,7 +204,7 @@ class ComplexFeaturizer(Featurizer):

		return np.asarray(features)

		def _featurize(self, complex: Tuple[str, str]):
		def _featurize(self, complex: Tuple[str, str], **kwargs):
		"""
		Calculate features for single mol/protein complex.

		@@ -234,7 +234,7 @@ class MolecularFeaturizer(Featurizer):
		The subclasses of this class require RDKit to be installed.
		"""

		def featurize(self, molecules, log_every_n=1000) -> np.ndarray:
		def featurize(self, molecules, log_every_n=1000, **kwargs) -> np.ndarray:
		"""Calculate features for molecules.

		Parameters
		@@ -278,7 +278,7 @@ class MolecularFeaturizer(Featurizer):
		new_order = rdmolfiles.CanonicalRankAtoms(mol)
		mol = rdmolops.RenumberAtoms(mol, new_order)

		features.append(self._featurize(mol))
		features.append(self._featurize(mol), **kwargs)
		except Exception as e:
		if isinstance(mol, Chem.rdchem.Mol):
		mol = Chem.MolToSmiles(mol)
		@@ -316,7 +316,7 @@ class MaterialStructureFeaturizer(Featurizer):

		def featurize(self,
		structures: Iterable[Union[Dict[str, Any], PymatgenStructure]],
		log_every_n: int = 1000) -> np.ndarray:
		log_every_n: int = 1000, **kwargs) -> np.ndarray:
		"""Calculate features for crystal structures.

		Parameters
		@@ -347,7 +347,7 @@ class MaterialStructureFeaturizer(Featurizer):
		try:
		if isinstance(structure, Dict):
		structure = Structure.from_dict(structure)
		features.append(self._featurize(structure))
		features.append(self._featurize(structure, **kwargs))
		except:
		logger.warning(
		"Failed to featurize datapoint %i. Appending empty array" % idx)
		@@ -380,7 +380,7 @@ class MaterialCompositionFeaturizer(Featurizer):
		"""

		def featurize(self, compositions: Iterable[str],
		log_every_n: int = 1000) -> np.ndarray:
		log_every_n: int = 1000, **kwargs) -> np.ndarray:
		"""Calculate features for crystal compositions.

		Parameters
		@@ -408,7 +408,7 @@ class MaterialCompositionFeaturizer(Featurizer):
		logger.info("Featurizing datapoint %i" % idx)
		try:
		c = Composition(composition)
		features.append(self._featurize(c))
		features.append(self._featurize(c, **kwargs))
		except:
		logger.warning(
		"Failed to featurize datapoint %i. Appending empty array" % idx)

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